NTR Case Study Project

Archival storage of non-DICOM and non-image data from the NTR in the

National Cancer Imaging Archive

Siemens Corporate ResearchBob Schwanke, John Pearson, Fabian

Moerchen, Philipp HusselsMarch, 2009

NTR (Network for Translational Research)

• NTR is the largest imaging translational research group funded by the NCI CIP (20 universities & companies)

• NTR validates clinical utility of new emerging imaging methods to be used in multi-center clinical trials

• NTR now entering the 2nd 5-year grant period

• Years 1-5 focused on optical imaging (NTR-OI)

• Years 6-10 generalize this beyond optical

• But translation imaging theme remains

• The new QIN grant from NCI CIP is organized like NTR(QIN – Quantitative Imaging Network, PAR 08-225)

Management of Experimental Data by the NTR-OI with SciPort

Current experimental data management and collaboration system (SciPort) used by the Network for Translational Research, Optical Imaging (NTR-OI) • Diverse categories of data.• Diverse file types.• Much of it non-standard & constantly

evolving with the imaging innovations

Purpose of this “NTR Case Study” Project

• This project is to “build two-way bridges” between the informatics efforts of NTR and caBIG

• NTR gains access to caBIG tools (as usual)• XIP, AIM, AVT, caGRID,…

• caBIG gains access to NTR data (as usual)• E.g., Optical/MR fused data for monitoring cancer therapy

• But caBIG also adapts useful tools developed by NTR• Imaging data management (SciPort); Image fusion/analysis (OMIRAD)

• First Step

• Publish NTR data directly to NCIA from SciPort• This enables the NTR to share data beyond their consortium, and provides

archival storage• Utilize the CTP “ZipObject” import scheme of NCIA

NTR-NCIA Bridge (1/3)

• SciPort document and attached files are stored in NCIA using CTP• Generate manifest.xml file with meta-data.• Generate dummy DICOM image with patient information.• Add non-DICOM and non-image data to ZIP object.• Send to Clinical Trial Processor (CTP).• Store in NCIA database.

DB2 MySQL

CTP

NTR-NCIA Bridge (2/3)

Database

Hibernate

NCIA caCOREAPI

Data Manager

Data Manager

CSM API

ProcessorsQuery, Result set, User Registration, Lookup Manager,

CSM, Export

Data TransferObject (DTO)

Java ServerFaces (JSF)

HibernateHibernate

DataAccessLayer

AuthenticationAuthentication

Hierarchy Management

Hierarchy Management

User Management

User Management

Schema Management

Schema Management

File UploaderFile Uploader

AnonymizerAnonymizer

Authoring ToolAuthoring Tool

SearchSearch

ReportReport

VisualizeVisualize

Com

mun

icat

ion

AP

IsC

omm

unic

atio

n A

PIsDocument Access ControlDocument Access Control

Anonymization Configurator

Anonymization Configurator Import ToolImport Tool

XML Database

Server(Metadata, Schemas)

XML Database

Server(Metadata, Schemas)

Data Folder(Files)

Data Folder(Files)

BrowseBrowse

UCIUCI

DartmouthDartmouth

MGHMGH

UPennUPenn NTROI SciPort Database

NCIA

Data Model Mapping

Data Model Mapping

Metadata PublishingMetadata Publishing

Image DataPublishing

Image DataPublishing

NTROI –NCIA Bridge

Summary to this Point

• Problem: – Translational Researchers need to share non-standard data from

emerging imaging systems, e.g., optical.– But NCIA is tailored to DICOM images with annotations.

• Solution: – Develop metadata models of all data (DICOM and other) with

SciPort– Upload data into NCIA as ZIP objects.

• Observations– Our generic approach can serve as a model for other

translational research networks with non conventional data formats.

– SciPort was used as it was already in use by the NTROI and is very general, so convenient for doing a proof-of-concept study

– But SciPort is not open-source at present…

Conclusion

Next steps

1. Create open-source bi-directional NCIA bridge– SciPort is not currently open source, so can’t be use “as is” in caBIG– SciPort-NCIA-bridge covers only upload, not download– Create an open source version of the tools demonstrated thus far that

would enable using the NCIA as a platform for sharing non-DICOM data:• Parse, package, and batch upload typical NTR data to NCIA.• Batch-download and unpack data for researchers.

2. Extend project to the new NTR partners – New NTR has replaced old NTROI, only Stanford remains.– Many new partners could benefit from the technology.– Fred Prior leads informatics working group of new NTR

3. Demonstrate large-scale feasibility by upload UCI data to NCIA – non-DICOM optical data on breast cancer.– Data should be parsed, unified and uploaded to the NCIA.

Conclusion